Microrna biomarkers for prognosis of patients with pancreatic cancer

Abstract

The present invention relates to prognostic micro RNA (miRNA) biomarkers based on a specific miRNA expression pattern, which can prove as a valuable prognostic tool to predict the survival of patients being diagnosed with pancreas cancer.

1 . A method for predicting the prognosis for a patient with pancreatic cancer, said method comprising measuring the expression level of at least one miRNA in a sample obtained from said individual, wherein the at least one miRNA is selected from the group consisting of
 a) miR-675, miR-212, miR-148a*, miR-187 and let-7g*; or   b) miR-675, miR-212, miR-148a* and miR-187; or   c) miR-675, miR-212, miR-148a* and let-7g*; or   d) miR-675, miR-212, miR-148a*, miR-187, miR-205, miR-944, miR-431, miR-194* and miR-769-5p; or   e) miR-675, miR-212, miR-148a*, miR-187, let-7g*, miR-205, miR-944, miR-431, miR-194*, miR-769-5p, miR-450b-5p, miR-222, miR-146a, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-449b and miR-330-5p; or   f) miR-675, miR-148a*, miR-450b-5p, miR-222 and miR-146a; or   g) miR-675, miR-148a*, miR-187, miR-205, miR-431, miR-194*, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-450b-5p, miR-449b and miR-330-5p;   h) miR-675, miR-148a* and miR-450b-5p; or   i) miR-675, miR-187, miR-205, miR-431, miR-194* and 148a*; or   j) miR-675 and miR-148a*, or   k) miR-675, miR222*, miR-29a*, miR-148a and miR-625.   wherein said method is a method for estimating the probability for a patient with pancreatic cancer of surviving for a certain time period, wherein the miRNA expression level of at least one of said miRNAs is indicative of said individual with pancreatic carcinoma surviving for a certain time period.   
     
     
         2 . The method according to  claim 1 , said method further comprising the step of obtaining a sample from an individual with pancreas cancer and/or extracting RNA from a sample collected from an individual with pancreas cancer. 
     
     
         3 . The method according to  claim 1 , said method further comprising the step of correlating the miRNA expression level of at least one of said miRNAs to a predetermined reference level. 
     
     
         4 . The method according to  claim 1 , said method further comprising the step of determining whether or not said sample is indicative of the individual having a certain predicted prognosis. 
     
     
         5 . The method according to  claim 1 , said method further comprising the step of obtaining prediction probabilities of between 0-1 for said sample. 
     
     
         6 . The method according to  claim 1 , wherein said time period is expressed as 3-months survival probability, 6-months survival probability, 9-months survival probability, 12-months survival/1-year survival probability, 2-years survival probability, 3-years survival probability, 4-years survival probability, 5-years survival probability, 6-years survival probability, 7-years survival probability, 8-years survival probability, 9-years survival probability or 10-years survival probability. 
     
     
         7 . The method according to  claim 1 , wherein said sample obtained from an individual is a tissue sample, such as a tissue sample from the pancreas, such as a tissue sample comprising pancreatic carcinoma cells. 
     
     
         8 . The method according to  claim 1 , wherein said sample obtained from an individual is a blood sample. 
     
     
         9 . The method according to  claim 1 , wherein said pancreatic carcinoma is pancreatic adenocarcinoma and/or ampullary adenocarcinoma. 
     
     
         10 . The method according to any of the preceding claims, comprising measuring the expression level of a group of miRNAs in a sample obtained from said individual, said group consisting of
 a) miR-675, miR-212, miR-148a*, miR-187 and let-7g*; or   b) miR-675, miR-212, miR-148a* and miR-187; or   c) miR-675, miR-212, miR-148a* and let-7g*; or   d) miR-675, miR-212, miR-148a*, miR-187, miR-205, miR-944, miR-431, miR-194* and miR-769-5p; or   e) miR-675, miR-212, miR-148a*, miR-187, let-7g*, miR-205, miR-944, miR-431, miR-194*, miR-769-5p, miR-450b-5p, miR-222, miR-146a, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-449b and miR-330-5p; or   f) miR-675, miR-148a*, miR-450b-5p, miR-222 and miR-146a; or   g) miR-675, miR-148a*, miR-187, miR-205, miR-431, miR-194*, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-450b-5p, miR-449b and miR-330-5p;   h) miR-675, miR-148a* and miR-450b-5p; or   i) miR-675, miR-187, miR-205, miR-431, miR-194* and 148a*; or   j) miR-675 and miR-148a*; or   k) miR-675, miR222*, miR-29a*, miR-148a and miR-625.   
     
     
         11 . The method according to any of the preceding claims, wherein the expression level of 2 miRNA is measured, such as 3 miRNAs, for example 4 miRNAs, such as 5 miRNAs, for example 6 miRNAs, such as 7 miRNAs, for example 8 miRNAs, such as 9 miRNAs, for example 10 miRNAs, such as 11 miRNAs, for example 12 miRNAs, such as 13 miRNAs, for example 14 miRNAs, such as 15 miRNAs, for example 16 miRNAs, such as 17 miRNAs, for example 18 miRNAs, such as 19 miRNAs, for example 20 miRNAs is measured. 
     
     
         12 . The method according to  claim 1 , wherein the expression level of one or more additional miRNAs is measured, said one or more additional miRNA having previously been identified in the literature as being of prognostic value. 
     
     
         13 . The method according to  claim 1 , wherein said method is used in combination with at least one additional prognostic method. 
     
     
         14 . The method according to  claim 1 , wherein the expression level of the at least one miRNA is determined by the microarray technique, or the quantitative polymerase chain reaction (QPCR) technique, or the northern blot technique, or the nuclease protection assay technique. 
     
     
         15 . The method according to  claim 1 , wherein the sample is extracted from an individual by fine-needle aspiration, or coarse-needle aspiration, or pancreatic surgery, or a pancreatic biopsy. 
     
     
         16 . A device for measuring the expression level of at least one miRNA in a sample, wherein said device comprises or consists of at least one probe or probe set for at least one miRNA selected from the group consisting of
 a) miR-675, miR-212, miR-148a*, miR-187 and let-7g*; or   b) miR-675, miR-212, miR-148a* and miR-187; or   c) miR-675, miR-212, miR-148a* and let-7g*; or   d) miR-675, miR-212, miR-148a*, miR-187, miR-205, miR-944, miR-431, miR-194* and miR-769-5p; or   e) miR-675, miR-212, miR-148a*, miR-187, let-7g*, miR-205, miR-944, miR-431, miR-194*, miR-769-5p, miR-450b-5p, miR-222, miR-146a, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-449b and miR-330-5p; or   f) miR-675, miR-148a*, miR-450b-5p, miR-222 and miR-146a; or   g) miR-675, miR-148a*, miR-187, miR-205, miR-431, miR-194*, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-450b-5p, miR-449b and miR-330-5p;   h) miR-675, miR-148a* and miR-450b-5p; or   i) miR-675, miR-187, miR-205, miR-431, miR-194* and 148a*; or   j) miR-675 and miR-148a*, or   k) miR-675, miR222*, miR-29a*, miR-148a and miR-625,
 wherein said device is used for characterising a sample obtained from a patient with pancreatic cancer. 
   
     
     
         17 . The device according to  claim 11 , wherein said device further comprises one or more probes or probe sets for one or more miRNA having previously been identified in the literature as being of prognostic value. 
     
     
         18 . The device according to  claims 11 - 12 , wherein said device is used in a method for estimating the probability for a patient with pancreatic cancer of surviving for a certain time period, said method comprising measuring the expression level of at least one miRNA in a sample obtained from said individual. 
     
     
         19 . The device according to  claim 11 , wherein said device is a microarray chip, a QPCR Microfluidic Card, QPCR tubes or a QPCR plate. 
     
     
         20 . A kit-of-parts comprising the device of  claim 11  and at least one additional component. 
     
     
         21 . The kit according to  claim 20 , wherein said additional component comprises means for extracting RNA such as miRNA, from a sample; reagents for performing microarray analysis; reagents for performing QPCR analysis; a computer program product according to  claim 23  and/or instructions for use of the device. 
     
     
         22 . A system for predicting the prognosis on an individual with pancreas cancer, comprising:
 i) means for analysing the miRNA expression profile of a sample obtained from said individual, and   ii) means for estimating the probability for a patient with pancreatic cancer of surviving for a certain time period,   wherein said miRNA expression profile comprises at least one miRNA selected from the group consisting of   a) miR-675, miR-212, miR-148a*, miR-187 and let-7g*; or   b) miR-675, miR-212, miR-148a* and miR-187; or   c) miR-675, miR-212, miR-148a* and let-7g*; or   d) miR-675, miR-212, miR-148a*, miR-187, miR-205, miR-944, miR-431, miR-194* and miR-769-5p; or   e) miR-675, miR-212, miR-148a*, miR-187, let-7g*, miR-205, miR-944, miR-431, miR-194*, miR-769-5p, miR-450b-5p, miR-222, miR-146a, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-449b and miR-330-5p; or   f) miR-675, miR-148a*, miR-450b-5p, miR-222 and miR-146a; or   g) miR-675, miR-148a*, miR-187, miR-205, miR-431, miR-194*, miR-23a*, miR-143*, miR-216a, miR-891a, miR-409-5p, miR-450b-5p, miR-449b and miR-330-5p;   h) miR-675, miR-148a* and miR-450b-5p; or   i) miR-675, miR-187, miR-205, miR-431, miR-194* and 148a*; or   j) miR-675 and miR-148a*, or   k) miR-675, miR222*, miR-29a*, miR-148a and miR-625   
     
     
         23 . A computer program product having a computer readable medium, said computer program product providing a system for predicting the prognosis of an individual, said computer program product comprising means for carrying out any of the steps of any of the methods according to  claim 22 .